Due to the high capacity of Trichoderma species in crop protection and promoting vegetative growth of plants, they are marketed as biofungicides and biofertilizers. Up to now, different secondary metabolites with antibiotic and antifugal activity have been characterized from Trichoderma spp. In this research, after consideration of the chemical compounds in Trichoderma atroviridae (6022) secondary metabolites based on GC/MS analysis, antifungal effect of one of the identified compounds (dibutyl phthalate) for control of soil borne fungi (Macrophomina phaseolina & Sclerotinia sclerotiorum) was confirmed. Since, isolation of the related compound by other methods is expensive and takes long time, so nanotechnology by Molecularly Imprinted Polymers (MIPs) was used. Now, this technique is used in biosensors, condensed drug, biochemical and membrane separation and also isolation of the bioactive ingredients of medicinal plants. For MIPs synthesis, pure “dibutyl phtalate”, was prepared and during precipitation polymerization, nanoporous MIPs were synthesized. In this procedure, first the template molecules are captured by functional monomers and then polymerization reaction in presense of cross linkers and initiator is carried out. After removal of the template molecules, nanoporous MIPs with binding capacity as equal 830 mg/g were synthesized. The resulting nanoporous MIPs have been used as stationary phase in column chromatography for extraction of “dibutyl phtalate” from Trichoderma atroviridae (6022) secondary metabolites. Due to low efficiency of chemical toxins for control of soil borne pathogens and environmental problems caused by their use and little amount of antifungal compounds in metabolites, these compounds can be separated and concentrated by this technology until the related technology can be used as a suitable alternative for chemical toxins.